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The von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone, Thr-Val linker variant, SUMO tag-free preparation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QAR 1TEL experimental model PDB 1SHT vWa experimental model PDB 1SHU 2QAR, 1SHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.1M HEPES, 2.0M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.43 49.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.882 α = 90 b = 100.882 β = 90 c = 49.754 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M Mirror: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2, Monochromator: Liquid nitrogen-cooled double crystal Si(111) 2022-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979460 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 19.87 99.56 0.05639 0.05799 0.01339 0.999 25.28 19 38098 27.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.658 99.13 0.9895 0.2253 0.939
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2QAR, 1SHU 1.6 19.87 1.38 38073 1951 99.63 0.1833 0.1821 0.2042 0.2202 41.57
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.754 f_angle_d 0.7583 f_chiral_restr 0.0474 f_plane_restr 0.0061 f_bond_d 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1936 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection autoPROC data reduction autoPROC data scaling PHASER phasing Coot model building